Related Research Articles
The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.
The Association of Biomolecular Resource Facilities (ABRF) is dedicated to advancing core and research biotechnology laboratories through research, communication, and education. ABRF members include over 2000 scientists representing 340 different core laboratories in 41 countries, including those in industry, government, academic and research institutions.
Rudolf Aebersold is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samples, in many cases via mass spectrometry. Ruedi Aebersold is a professor of Systems biology at the Institute of Molecular Systems Biology (IMSB) in ETH Zurich. He was one of the founders of the Institute for Systems Biology in Seattle, Washington, where he previously had a research group.
The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra.
Shotgun proteomics refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing pattern of a shotgun. The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. Tandem mass spectrometry is then used to identify the peptides.
An isotope-coded affinity tag (ICAT) is an in-vitro isotopic labeling method used for quantitative proteomics by mass spectrometry that uses chemical labeling reagents. These chemical probes consist of three elements: a reactive group for labeling an amino acid side chain, an isotopically coded linker, and a tag for the affinity isolation of labeled proteins/peptides. The samples are combined and then separated through chromatography, then sent through a mass spectrometer to determine the mass-to-charge ratio between the proteins. Only cysteine containing peptides can be analysed. Since only cysteine containing peptides are analysed, often the post translational modification is lost.
The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification.
OpenMS is an open-source project for data analysis and processing in mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, MacOS and Linux.
Selected reaction monitoring (SRM), also called multiple reaction monitoring (MRM), is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion product of a fragmentation reaction of the precursor ions is selected in the second mass spectrometer stage for detection.
Hui Zhang is a professor of Pathology at Johns Hopkins University. She specializes in analysis of glycoproteins and other protein modifications on the proteome scale. Her most cited article is Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry.
The PRIDE is a public data repository of mass spectrometry (MS) based proteomics data, and is maintained by the European Bioinformatics Institute as part of the Proteomics Team.
The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization. Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome.
Albert J.R. Heck is a Dutch scientist and professor at Utrecht University, the Netherlands in the field of mass spectrometry and proteomics. He is known for his work on technologies to study proteins in their natural environment, with the aim to understand their biological function. Albert Heck was awarded the Spinoza Prize in 2017, the highest scientific award in the Netherlands.
Ronald Charles Beavis is a Canadian protein biochemist, who has been involved in the application of mass spectrometry to protein primary structure, with applications in the fields of proteomics and analytical biochemistry. He has developed methods for measuring the identity and post-translational modification state of proteins obtained from biological samples using mass spectrometry. He is currently best known for developing new methods for analyzing proteomics data and applying the results of these methods to problems in computational biology.
Anne-Claude Gingras is a senior investigator at Lunenfeld-Tanenbaum Research Institute, and a professor in the department of molecular genetics at the University of Toronto. She is an expert in mass spectrometry based proteomics technology that allows identification and quantification of protein from various biological samples.
Olga Vitek is a biostatistician and computer scientist specializing in bioinformatics, proteomics, mass spectrometry, causal inference of biological function, and the development of open-source software for statistical analysis in these areas. She is a professor in the College of Science and Khoury College of Computer Sciences of Northeastern University.
Catherine E. Costello is the William Fairfield Warren distinguished professor in the department of biochemistry, Cell Biology and Genomics, and the director of the Center for Biomedical Mass Spectrometry at the Boston University School of Medicine.
Paola Picotti is an Italian biologist who is Professor for Molecular Systems Biology at ETH Zürich. She is Deputy Head of the Institute for Molecular Systems Biology. Her research investigates how the conformational changes of proteins impact cellular networks. She was awarded the 2020 ETH Zürich Rössler Prize and the 2019 EMBO Gold Medal.
References
- ↑ Desiere, Frank; Deutsch, Eric W.; Nesvizhskii, Alexey I.; Mallick, Parag; King, Nichole L.; Eng, Jimmy K.; Aderem, Alan; Boyle, Rose; Brunner, Erich; Donohoe, Samuel; Fausto, Nelson; Hafen, Ernst; Hood, Lee; Katze, Michael G.; Kennedy, Kathleen A.; Kregenow, Floyd; Lee, Hookeun; Lin, Biaoyang; Martin, Dan; Ranish, Jeffrey A.; Rawlings, David J.; Samelson, Lawrence E.; Shiio, Yuzuru; Watts, Julian D.; Wollscheid, Bernd; Wright, Michael E.; Yan, Wei; Yang, Lihong; Yi, Eugene C.; Zhang, Hui; Aebersold, Ruedi (2005). "Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry". Genome Biology. 6 (1): –9. doi: 10.1186/gb-2004-6-1-r9 . ISSN 1474-760X. PMC 549070 . PMID 15642101.